Coexpression cluster:C424

Full id: C424_Hepatocyte_liver_Synoviocyte_tenocyte_Fibroblast_Adipocyte_Cardiac

Phase1 CAGE Peaks

Hg19::chr11:57367575..57367593,+	p7@SERPING1
Hg19::chr12:7167997..7168040,+	p1@C1S
Hg19::chr12:7168041..7168058,+	p2@C1S
Hg19::chr12:7169832..7169844,+	p8@C1S
Hg19::chr12:7169889..7169902,+	p6@C1S
Hg19::chr12:7169907..7169929,+	p5@C1S
Hg19::chr12:7170214..7170228,+	p9@C1S
Hg19::chr12:7170229..7170249,+	p10@C1S
Hg19::chr12:7171627..7171662,+	p4@C1S
Hg19::chr12:7175756..7175804,+	p@chr12:7175756..7175804 +
Hg19::chr12:7177634..7177646,+	p@chr12:7177634..7177646 +
Hg19::chr12:7177786..7177801,+	p@chr12:7177786..7177801 +
Hg19::chr12:7177864..7177876,+	p@chr12:7177864..7177876 +
Hg19::chr12:7187896..7187912,-	p@chr12:7187896..7187912 -
Hg19::chr12:7241517..7241547,-	p@chr12:7241517..7241547 -
Hg19::chr12:7241961..7241984,-	p@chr12:7241961..7241984 -
Hg19::chr12:7242235..7242247,-	p@chr12:7242235..7242247 -
Hg19::chr12:7242281..7242299,-	p@chr12:7242281..7242299 -
Hg19::chr12:7242779..7242821,-	p9@C1R
Hg19::chr12:7244160..7244201,-	p6@C1R
Hg19::chr12:7244222..7244240,-	p8@C1R
Hg19::chr12:7244261..7244276,-	p12@C1R
Hg19::chr12:7245018..7245073,-	p1@C1R
Hg19::chr12:7261772..7261874,-	p1@C1RL

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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p.value	FDR	nGenes	nPathway	Name
5.39695550498319e-08	1.13875761155145e-05	3	69	Complement and coagulation cascades (KEGG):04610
2.26219774485948e-05	0.00286394234499211	2	56	Staphylococcus aureus infection (KEGG):05150
0.000138328844145387	0.0145936930573384	2	138	Systemic lupus erythematosus (KEGG):05322
2.79572408770279e-06	0.000442423336878966	2	20	Complement Activation, Classical Pathway (Wikipathways):WP545
2.27747619344567e-08	7.20821215225554e-06	3	52	Complement and Coagulation Cascades (Wikipathways):WP558
1.78259609854325e-08	7.20821215225554e-06	3	48	{FCGR2B,50} (Static Module):NA

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0006508	proteolysis	0.0132525917284209
GO:0004252	serine-type endopeptidase activity	0.0132525917284209
GO:0008236	serine-type peptidase activity	0.0132525917284209
GO:0017171	serine hydrolase activity	0.0132525917284209
GO:0004175	endopeptidase activity	0.033273032044513
GO:0006958	complement activation, classical pathway	0.033273032044513
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.033273032044513
GO:0006956	complement activation	0.033273032044513
GO:0002541	activation of plasma proteins during acute inflammatory response	0.033273032044513
GO:0016064	immunoglobulin mediated immune response	0.033273032044513
GO:0019724	B cell mediated immunity	0.033273032044513
GO:0008233	peptidase activity	0.033273032044513
GO:0002253	activation of immune response	0.033273032044513
GO:0002449	lymphocyte mediated immunity	0.033273032044513
GO:0006959	humoral immune response	0.033273032044513
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.033273032044513
GO:0002250	adaptive immune response	0.033273032044513
GO:0002443	leukocyte mediated immunity	0.033273032044513
GO:0002526	acute inflammatory response	0.033273032044513
GO:0050778	positive regulation of immune response	0.033273032044513
GO:0002684	positive regulation of immune system process	0.033273032044513
GO:0050776	regulation of immune response	0.033273032044513
GO:0007596	blood coagulation	0.033273032044513
GO:0002682	regulation of immune system process	0.033273032044513
GO:0050817	coagulation	0.033273032044513
GO:0007599	hemostasis	0.033273032044513
GO:0051240	positive regulation of multicellular organismal process	0.033273032044513
GO:0002252	immune effector process	0.033605128731863
GO:0045087	innate immune response	0.0336202558677497
GO:0050878	regulation of body fluid levels	0.0355140395553653
GO:0042060	wound healing	0.0355140395553653
GO:0044267	cellular protein metabolic process	0.0355140395553653
GO:0044260	cellular macromolecule metabolic process	0.0357225886968076
GO:0019538	protein metabolic process	0.0379340249739084
GO:0008015	blood circulation	0.0379340249739084
GO:0003013	circulatory system process	0.0379340249739084
GO:0004867	serine-type endopeptidase inhibitor activity	0.0387405217571341

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	9.03e-20	180
fibroblast	4.12e-14	75
muscle precursor cell	2.51e-10	57
myoblast	2.51e-10	57
multi-potent skeletal muscle stem cell	2.51e-10	57
muscle cell	5.21e-10	54
contractile cell	8.37e-10	59
electrically responsive cell	6.38e-09	60
electrically active cell	6.38e-09	60
fat cell	1.17e-07	15
smooth muscle cell	1.63e-07	42
smooth muscle myoblast	1.63e-07	42

Uber Anatomy

Ontology term	p-value	n
multi-tissue structure	4.12e-20	347
organism subdivision	2.80e-19	365
multi-cellular organism	3.51e-17	659
trunk mesenchyme	1.37e-14	143
anatomical system	7.88e-14	625
anatomical group	1.58e-13	626
mesenchyme	5.25e-13	238
entire embryonic mesenchyme	5.25e-13	238
anatomical cluster	9.79e-13	286
trunk	1.41e-12	216
somite	4.58e-12	83
paraxial mesoderm	4.58e-12	83
presomitic mesoderm	4.58e-12	83
presumptive segmental plate	4.58e-12	83
trunk paraxial mesoderm	4.58e-12	83
presumptive paraxial mesoderm	4.58e-12	83
muscle tissue	6.23e-12	63
musculature	6.23e-12	63
musculature of body	6.23e-12	63
adult organism	1.13e-11	115
skeletal muscle tissue	3.12e-11	61
striated muscle tissue	3.12e-11	61
myotome	3.12e-11	61
dermomyotome	8.64e-11	70
embryo	1.03e-09	612
organ	1.28e-09	511
anatomical conduit	1.47e-09	241
multilaminar epithelium	1.77e-09	82
cell layer	1.86e-09	312
embryonic structure	1.90e-09	605
developing anatomical structure	1.90e-09	605
epithelium	2.19e-09	309
germ layer	3.14e-09	604
embryonic tissue	3.14e-09	604
presumptive structure	3.14e-09	604
epiblast (generic)	3.14e-09	604
surface structure	1.23e-08	95
primary circulatory organ	4.89e-08	27
unilaminar epithelium	7.35e-08	138
heart	2.20e-07	24
primitive heart tube	2.20e-07	24
primary heart field	2.20e-07	24
anterior lateral plate mesoderm	2.20e-07	24
heart tube	2.20e-07	24
heart primordium	2.20e-07	24
cardiac mesoderm	2.20e-07	24
cardiogenic plate	2.20e-07	24
heart rudiment	2.20e-07	24
digestive system	3.42e-07	155
digestive tract	3.42e-07	155
primitive gut	3.42e-07	155
epithelial tube	7.27e-07	118

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
STAT3#6774	7	3.06817729083665	0.00565146722640425	0.0255236145149593

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.